By the time I was woking on this project Google Charts was fragmented into 2 different libraries, Google Image charts and Google Visualization API.
My project was to draw a dashboard with multiple charts and connect them to data sources that collected the charts data on the backend. So every time you loaded the dashboard it fired multiple AJAX calls one for each chart's data.
Flot was very easy to work with, the interface to load data is simple and makes sense. It offered good options to customize charts. It offered Mixed charts where you could have lines and bars on the same chart. That was the only reason I brought flot to the mix, there was no way to draw charts using bars and lines on Google Charts back then.
Google Charts on the other hand was a little bit harder to work with. The interface to input data is less obvious and has some strange decisions. Important to notice that Google Charts also defines a protocol to load data into charts, the protocol was called "wire protocol" back then but was renamed to "Chart Tools Datasource Protocol" currently on version 0.6. Sometimes the chart design was inconsistent and that was apparent when you had a bunch of different chart types on the same page. The Geo charts also had a weird behavior, different from most other charts, possibly because they were rendered using flash. The protocol Google establishes for chart data is hard to get started but once you integrate with it is very easy to change the visualization and creates good structure.
Google Charts got a big update a couple weeks ago, the previous version are being deprecated and all charts are now rendered using HTML5 techniques, most of the time SVG. The protocol also got a big update and fixed a lot of bugs that made my life somewhat miserable weeks ago. Now it also supports mixed charts (bars and lines), so I don't need flot anymore.
I'm in the process of creating another dashboard now, and I've been using Google Charts only this time.
My advice is that if you're planning to draw only a couple of charts and flotr2 does the work go with it. It's easier to work with and lighter.
If you're building something that depends on charts a lot go with Google Charts. The protocol will come handy and it has some helpers to connect to backend data sources and Google Spreadsheets built-in.
If you need to create a product that relies on the charting library too much you probably want to support more than one charting library and possibly have the option to switch the library on the fly. The deprecation of the previous Charting library. The deprecation policy for Google Charts may be a little frightening.